Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6389
Trapped Gene
Elavl1 (ENSMUSG00000040028)
Vector Insertion
Chr 8: 4305031 - 4311598
Public Clones YHC020 (baygenomics) PST22797-NR (escells)
Private Clones OST242095 (lexicon) OST66611 (lexicon) OST56811 (lexicon)
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000229444 (Chr8:4311599..4311786 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACGAAGTCTGTTCAGCAGCA Chr8:4311644..4311663 59.78 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000229444 (Chr8:4311599..4311786 -)
Downstram Exon
ENSMUSE00000229435 (Chr8:4304927..4305030 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACGAAGTCTGTTCAGCAGCA Chr8:4311644..4311663 59.78 50 GTCTCAAGCCGTTCAGTGTG Chr8:4304925..4304944 59.47 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000638320 Chr8:4324886..4325086 No primer for this exon
upstream ENSMUSE00000706646 Chr8:4324886..4324906 No primer for this exon
upstream ENSMUSE00000706645 Chr8:4312557..4312614 No primer for this exon
upstream ENSMUSE00000229444 Chr8:4311599..4311786 ACGAAGTCTGTTCAGCAGCA Chr8:4311644..4311663 59.78 50

*** Putative Vector Insertion (Chr 8: 4305031 - 4311598) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000229435 Chr8:4304927..4305030 GTCTCAAGCCGTTCAGTGTG Chr8:4304925..4304944 59.47 55
downstream ENSMUSE00000229429 Chr8:4301685..4301838 AGTTGATGATTCGCCCAAAC Chr8:4301690..4301709 59.94 45
downstream ENSMUSE00000278547 Chr8:4295336..4295561 CTGCTTCTGACCGTTTGTCA Chr8:4295489..4295508 60.03 50
downstream ENSMUSE00000638319 Chr8:4288347..4289924 ACAGAACCCCAAACGTCAAG Chr8:4288409..4288428 60.01 50
downstream ENSMUSE00000706644 Chr8:4288344..4289924 ACAGAACCCCAAACGTCAAG Chr8:4288409..4288428 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CATTCCTGTAATCGCCTTGC Chr8:4308535..4308555 60.61 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACGTCTCATTCCTGCGTGAC Chr8:4308541..4308561 61.29 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GCCTCTCAGCTCTCATTCCA Chr8:4308770..4308790 60.65 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GCCTCTCAGCTCTCATTCCA Chr8:4308770..4308790 60.65 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040028